Why 3 D to 2 D?
well this has made because I have too encode one movie sterioscopic "3 D" to 2 D my system is not good (I don't have all hardware). So I add to found a solution for encode 3 D to 2 D, I goggle it but only found how to encode (convert) to 2 D to 3 D. Them came to me the idea try this on MEgui, well the result has amazing, but this as made on Windows, and I want try to on Ubuntu in Avidemux, so I use the sample of 3dvision-blog.com to make this "how to".

"how to"
This is on Ubuntu 10.10 64bit this sample of the "how to" take 30min to encode on my laptop 2hz coredue 2GB memory, your miles may very.
Start, go to Applications, Sound & Video, Avidemux, (if you don't have this install it, using Software centre),

after you choose the video codec, you can use configure, for the encode,

encode by ["encode mode" (single or dual pass)], ["target size" (if is for a single dvd 4Gb], or ["quantizer" (big number to low, from 51 to 0, but 51 bad quality 0 best quality).

by default the max ref. frames are 3, but I use 4, don't go over 6, software like multiAVC will claim about it.

"filters" menu where we need change a few thing for the best end result,

on transform filter use resize, crop & resize but this is only necessary only like this case the sample is 3000x800 so resize first to 1280x720, them crop 640 & resize again to 1280x720,

3000x800 to 1280x720

destination 16:9 and lanczos3, [on MEgui is lanczos4]

screenshot of correct sise 1280x720, now crop,

half of 1280 is 640 input that on with and click enter (return key),

choose from left or right to crop in to half,

them resize again to 1280x720, from the filters menu you have to use for this first resise MPayer,then crop and last resize with avisynth,

screenshot after all the settings apply,

save the file for Avidemux start the encode, my is avt.mkv, in Avidemux you have to add .mkv to the end of the file and after the encode use the MKmerge to change the internal name of the file "tag" for the name that you want.

Mkmerge gui

in Mkmerge, file segment title, under global tab is "Avidemux", change for the name that you want or clear it, is up to you. MEgui you don't need do this, so that it I hope this will help someone.
The end result to compare here: http://dl.dropbox.com/u/16165934/avt.mkv

Here's what I figured you were trying to say:1. I opened a 3D side-by-side MKV file into avidemux on Centos6 using the command:AviDemux:File->Open->3d.mkv2. AviDemux:File->Information showed the original file to be of the format:- Video Codec 4CC = AVC1/Image Size = 1920x1080- Audio Codec = DTS/Audio Channels = 63. Since 1920 pixels divided in half is 960 pixels, I cropped to the left half using the command:Avidemux: Video->Filters->Transform->Crop->{top=0,bottom=0,left=0,right=960}4. I resized that cropped portion back to 1920 pixels using this command:Avidemux:Video->Filters->Transform->MPlayer resize->"+"->"Lock aspect ratio" was changed from "on" to "off" & "Resize Dimensions" were changed from 960x1080 to 1920x1080.5. I re-encoded the result using the command:Avidemux:File->Save->Save Video->Filename=2d.avi